Variant report

Variant	rs2120103
Chromosome Location	chr3:105519316-105519317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11919893	0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs11926659	0.90[ASN][1000 genomes]
rs12054270	0.84[AMR][1000 genomes]
rs12497428	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs12632980	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs13090949	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs13326550	0.90[ASN][1000 genomes]
rs13433776	0.89[ASN][1000 genomes]
rs1443100	1.00[CEU][hapmap]
rs1503923	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16851512	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs16851553	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs16851596	0.93[ASN][1000 genomes]
rs16851673	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap]
rs16851705	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16851706	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1814078	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1867194	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes]
rs2028598	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs2028599	0.90[AMR][1000 genomes]
rs2055559	1.00[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs2301028	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs2301034	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs2301035	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs3213928	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs34360428	0.90[AMR][1000 genomes]
rs3772522	0.84[AMR][1000 genomes]
rs3772525	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs4469007	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs4894956	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs62256353	0.92[AMR][1000 genomes]
rs62261460	0.90[AMR][1000 genomes]
rs62261462	0.90[AMR][1000 genomes]
rs62261487	0.90[AMR][1000 genomes]
rs62261489	0.90[AMR][1000 genomes]
rs62261491	0.90[AMR][1000 genomes]
rs62261492	0.90[AMR][1000 genomes]
rs62261493	0.90[AMR][1000 genomes]
rs62261495	0.90[AMR][1000 genomes]
rs62261496	0.90[AMR][1000 genomes]
rs62261497	0.90[AMR][1000 genomes]
rs62261498	0.90[AMR][1000 genomes]
rs62261499	0.90[AMR][1000 genomes]
rs62261538	0.92[AMR][1000 genomes]
rs62261539	0.92[AMR][1000 genomes]
rs62263057	0.81[AMR][1000 genomes]
rs62263169	0.92[AMR][1000 genomes]
rs62263170	0.92[AMR][1000 genomes]
rs62264260	0.83[AMR][1000 genomes]
rs6437616	0.89[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs6766168	0.84[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs6776593	0.93[ASN][1000 genomes]
rs6780432	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs6809776	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs7619706	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs7628896	0.90[AMR][1000 genomes]
rs7631219	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs7634195	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7638504	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7641527	0.81[AMR][1000 genomes]
rs7650046	1.00[CEU][hapmap]
rs894541	0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs964173	0.88[AMR][1000 genomes]
rs9657924	1.00[CEU][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs971109	1.00[CEU][hapmap];0.92[AMR][1000 genomes]
rs9811776	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs9814582	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs9837243	0.93[ASN][1000 genomes]
rs9838755	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs9846445	0.93[ASN][1000 genomes]
rs9856147	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs9872895	0.89[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
4	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:105509800-105527800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:105510600-105521200	Weak transcription	Fetal Brain Male	brain
7	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
8	chr3:105511800-105520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:105512000-105520600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:105512200-105520200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:105512200-105520400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
14	chr3:105512400-105524400	Weak transcription	NHLF	lung
15	chr3:105512600-105520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:105512600-105524000	Weak transcription	HSMMtube	muscle
17	chr3:105512600-105524600	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:105512600-105525200	Weak transcription	HSMM	muscle
19	chr3:105514400-105521600	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:105515400-105528200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:105515400-105539000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:105515800-105521600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr3:105516000-105519400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:105516000-105521600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:105516000-105521600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:105516200-105522200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:105516400-105519400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:105516400-105521000	Enhancers	Primary T cells from cord blood	blood
29	chr3:105516400-105521800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:105516600-105519400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:105516600-105519400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:105516600-105519800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:105516600-105522000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:105516600-105523000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:105516800-105519800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr3:105517200-105519400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:105517400-105519600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:105517400-105519800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:105517800-105519600	Genic enhancers	Osteobl	bone
40	chr3:105517800-105519800	Weak transcription	Fetal Heart	heart
41	chr3:105517800-105520400	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:105517800-105520800	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:105517800-105521000	Weak transcription	NH-A	brain
44	chr3:105517800-105522000	Enhancers	Primary B cells from cord blood	blood
45	chr3:105517800-105522200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:105517800-105524800	Weak transcription	A549	lung
47	chr3:105517800-105525400	Weak transcription	Fetal Intestine Large	intestine
48	chr3:105517800-105527800	Weak transcription	Fetal Kidney	kidney
49	chr3:105517800-105528200	Weak transcription	Brain Substantia Nigra	brain
50	chr3:105517800-105528400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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